Deep Learning in R Programming

Deep Learning is a type of Artificial Intelligence or AI function that tries to imitate or mimic the working principle of a human brain for data processing and pattern creation for decision-making purposes. It is a subset of ML or machine learning in an AI that owns or have networks that are capable of unsupervised learning from data that are unlabeled or unstructured. Deep learning can also be called as deep neural learning or deep neural network. Deep Learning AI is capable of learning without human supervision, drawing from any kind of data. Being a subset of machine learning, deep learning utilizes an artificial neural network of a hierarchical level in order to carry out the machine learning procedures or processes. With the help of deep learning, we can unravel a huge amount of data that is unstructured in nature. For humans, that would take decades normally to understand and process it. 

Implementation in R

R Language has been decorated with many deep learning packages in CRAN in the due course of time. Some of these packages are as follows :

R Package Name	Description
nnet	Used for feed-forward NN having a single hidden layer  or for a multinomial log-linear model.
neuralnet	Used in training of NN using back-propagation.
h2o	It is an R Scripting functionality for H2O
RSNNS	An interface to the Stuttgart NN Simulator.
tensorflow	An interface for the TensorFlow.
deepnet	It is a toolkit in R for deep learning.
darch	It is a package for the Deep Architectures and  Restricted Boltzmann Machines.
rnn	A package to implement Recurrent NN.
FCNN4R	Interface for the FCNN library which allows user-extensible ANNs.
rcppdl	Used to implement machine learning.
deepr	Based on darch and deepnet, it is a package to  enhance the streamline the training, predicting process and fine-tuning for deep learning.

Recently Keras, kerasR, and keras are also used for deep learning purposes. Here we will be using the deepnet package for implementing deep learning. Let’s proceed with the step-by-step procedure of the implementation. The entire implementation process can be divided into the following steps:

Step 1: Installing and Loading the Packages 

Before proceeding with the implementations, install the required packages. For our implementation, we will require the deepnet and mlbench packages. To install these packages from the R Console use the install.packages() command. On successful installation of these packages, load them in the R Script using the library() command as follows:

R

# Deep Learning in R
# loading the required packages
library(mlbench)
library(deepnet)

Step 2: Choosing Dataset 

Now the task is to select a proper dataset for the implementation. Here let’s work with the Breast Cancer Dataset under the mlbench package. Include the data set in the R Script as follows:

R

# Deep learning in R
# loading the required packages
library(mlbench)
library(deepnet)
data("BreastCancer")

# Clean off rows with missing data
BreastCancer = BreastCancer[which(complete.cases(BreastCancer)
                                  == TRUE),]
head(BreastCancer)
names(BreastCancer)

Output:

> head(BreastCancer)
       Id Cl.thickness Cell.size Cell.shape Marg.adhesion Epith.c.size Bare.nuclei Bl.cromatin Normal.nucleoli Mitoses     Class
1 1000025            5         1          1             1            2           1           3               1       1    benign
2 1002945            5         4          4             5            7          10           3               2       1    benign
3 1015425            3         1          1             1            2           2           3               1       1    benign
4 1016277            6         8          8             1            3           4           3               7       1    benign
5 1017023            4         1          1             3            2           1           3               1       1    benign
6 1017122            8        10         10             8            7          10           9               7       1 malignant
> names(BreastCancer)
 [1] "Id"              "Cl.thickness"    "Cell.size"       "Cell.shape"      "Marg.adhesion"   "Epith.c.size"    "Bare.nuclei"    
 [8] "Bl.cromatin"     "Normal.nucleoli" "Mitoses"         "Class" 

Step 3: Applying the deepnet package to the dataset

Apply the deep learning package on the chosen dataset. Here, create a set of features for independent variables, and create the dependent variable.

R

# Deep learning in R
# Loading the required packages
library(mlbench)
library(deepnet)
data("BreastCancer")

# Clean off rows with missing data
BreastCancer = BreastCancer[which(complete.cases(BreastCancer)
                                  == TRUE),]

head(BreastCancer)
names(BreastCancer)
y = as.matrix(BreastCancer[, 11])
y[which(y == "benign")] = 0
y[which(y == "malignant")] = 1
y = as.numeric(y)
x = as.numeric(as.matrix(BreastCancer[, 2:10]))
x = matrix(as.numeric(x), ncol = 9)

Step 4: Modeling NN

Apply nn.train() function under the deepnet package in order to model the neural network.

R

# Deep learning in R
# Loading packages in R
library(mlbench)
library(deepnet)
data("BreastCancer")

# Clean off rows with missing data
BreastCancer = BreastCancer[which(complete.cases(BreastCancer)
                                  == TRUE),]

head(BreastCancer)
names(BreastCancer)
y = as.matrix(BreastCancer[, 11])
y[which(y == "benign")] = 0
y[which(y == "malignant")] = 1
y = as.numeric(y)
x = as.numeric(as.matrix(BreastCancer[, 2:10]))
x = matrix(as.numeric(x), ncol = 9)

# Applying nn.train() function
nn <- nn.train(x, y, hidden = c(5))
yy = nn.predict(nn, x)
print(head(yy))

Output:

> print(head(yy))
          [,1]
[1,] 0.2743838
[2,] 0.4130857
[3,] 0.2892783
[4,] 0.4232022
[5,] 0.2817078
[6,] 0.4526502

Step 5: Creating a confusion matrix

Retrieve the neural network’s output and then convert it into class. In order to create a confusion matrix, use the table() function. Also check the accuracy of the confusion matrix by dividing the sum of the diagonal elements with the total count or sum of all the numbers.

R

# Deep Learning in R
# Loading required packages
library(mlbench)
library(deepnet)
data("BreastCancer")

# Clean off rows with missing data
BreastCancer = BreastCancer[which(complete.cases(BreastCancer)
                                  == TRUE),]

head(BreastCancer)
names(BreastCancer)
y = as.matrix(BreastCancer[, 11])
y[which(y == "benign")] = 0
y[which(y == "malignant")] = 1
y = as.numeric(y)
x = as.numeric(as.matrix(BreastCancer[, 2:10]))
x = matrix(as.numeric(x), ncol = 9)

# Applying nn.train() method
nn <- nn.train(x, y, hidden = c(5))
yy = nn.predict(nn, x)
print(head(yy))
yhat = matrix(0,length(yy), 1)
yhat[which(yy > mean(yy))] = 1
yhat[which(yy <= mean(yy))] = 0

# Applying table() function
cm = table(y, yhat)
print(cm)
print(sum(diag(cm))/sum(cm))

Output:

> print(cm)
   yhat
y     0   1
  0 425  19
  1   4 235
> print(sum(diag(cm))/sum(cm))
[1] 0.966325